1-222247176-A-T

Position:

• chr1-222247176-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416510.1(ENSG00000236230):​n.168-28687T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,112 control chromosomes in the GnomAD database, including 37,748 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (37748 hom., cov: 32)
• Consequence: ENST00000416510.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000416510.1	n.168-28687T>A		intron_variant, non_coding_transcript_variant		1
	ENST00000652067.1	n.420-58450T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106054 AN: 151994 Hom.: 37698 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.685

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.698 AC: 106161 AN: 152112 Hom.: 37748 Cov.: 32 AF XY: 0.693 AC XY: 51542 AN XY: 74376

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.686

Alfa AF: 0.556 Hom.: 1467

Bravo AF: 0.705

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs158724; hg19: chr1-222420518;